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PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry
Author(s) -
Ma Bin,
Zhang Kaizhong,
Hendrie Christopher,
Liang Chengzhi,
Li Ming,
DohertyKirby Amanda,
Lajoie Gilles
Publication year - 2003
Publication title -
rapid communications in mass spectrometry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.528
H-Index - 136
eISSN - 1097-0231
pISSN - 0951-4198
DOI - 10.1002/rcm.1196
Subject(s) - tandem mass spectrometry , chemistry , software , mass spectrometry , peptide , computational biology , tandem , peptide sequence , sequence (biology) , combinatorial chemistry , chromatography , computer science , biochemistry , biology , gene , materials science , composite material , programming language
A number of different approaches have been described to identify proteins from tandem mass spectrometry (MS/MS) data. The most common approaches rely on the available databases to match experimental MS/MS data. These methods suffer from several drawbacks and cannot be used for the identification of proteins from unknown genomes. In this communication, we describe a new de novo sequencing software package, PEAKS, to extract amino acid sequence information without the use of databases. PEAKS uses a new model and a new algorithm to efficiently compute the best peptide sequences whose fragment ions can best interpret the peaks in the MS/MS spectrum. The output of the software gives amino acid sequences with confidence scores for the entire sequences, as well as an additional novel positional scoring scheme for portions of the sequences. The performance of PEAKS is compared with Lutefisk, a well‐known de novo sequencing software, using quadrupole‐time‐of‐flight (Q‐TOF) data obtained for several tryptic peptides from standard proteins. Copyright © 2003 John Wiley & Sons, Ltd.